Variant report

Variant	rs12409933
Chromosome Location	chr1:10395530-10395531
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:10388606..10392277-chr1:10395512..10398907,3	K562	blood:

Extended variants
information (count: 149 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:143)

rs_ID	r²[population]
rs1002076	0.88[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs1013952	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1013953	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10492971	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10492972	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10492973	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1065828	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10864449	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10864450	0.82[ASN][1000 genomes]
rs10864453	0.91[ASN][1000 genomes]
rs11121535	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11121537	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11121539	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11121541	0.86[ASN][1000 genomes]
rs11121544	0.81[AMR][1000 genomes]
rs11121545	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11121551	0.88[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs11121560	0.84[EUR][1000 genomes]
rs1138791	0.88[EUR][1000 genomes]
rs11576459	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11576866	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs11578788	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs11579365	0.85[EUR][1000 genomes]
rs11580789	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11580854	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11582123	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11584023	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11585760	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs11585794	0.82[EUR][1000 genomes]
rs11586842	0.89[EUR][1000 genomes]
rs11587309	0.84[EUR][1000 genomes]
rs11587495	0.83[EUR][1000 genomes]
rs11587854	0.84[EUR][1000 genomes]
rs12117635	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12119477	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs12120042	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12120191	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12122029	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12125535	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12127604	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12128374	0.84[ASN][1000 genomes]
rs12130220	0.84[AMR][1000 genomes]
rs12130563	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12131441	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12132134	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12137880	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12139981	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12141201	0.84[EUR][1000 genomes]
rs12141246	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12141416	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12403465	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12406943	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12409137	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12409754	0.84[EUR][1000 genomes]
rs12722830	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12725210	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12734068	0.82[AMR][1000 genomes]
rs12734551	0.81[AMR][1000 genomes]
rs12737239	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12738317	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12753426	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12757288	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1467653	0.86[ASN][1000 genomes]
rs1536263	0.81[AMR][1000 genomes]
rs1538557	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1555849	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1556916	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1556917	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17034643	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17034821	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17396973	0.82[ASN][1000 genomes]
rs17401924	0.81[AMR][1000 genomes]
rs17401966	0.81[AMR][1000 genomes]
rs17402762	0.86[ASN][1000 genomes]
rs17410217	0.94[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17410793	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2004034	0.81[AMR][1000 genomes]
rs2039778	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2105212	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2148152	0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2182326	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2185252	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2276100	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34215045	0.81[AMR][1000 genomes]
rs34225619	0.85[AMR][1000 genomes]
rs34565762	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs34636442	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35388505	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35716098	0.80[EUR][1000 genomes]
rs35759975	0.84[EUR][1000 genomes]
rs35850116	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3737155	0.84[EUR][1000 genomes]
rs3748575	0.84[ASN][1000 genomes]
rs3748577	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3748578	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs3748579	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3753037	0.81[AMR][1000 genomes]
rs4240911	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4333852	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4475756	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4529713	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4623	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4845931	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4845932	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4846197	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4846205	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4846206	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4846207	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4846209	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4846211	0.81[ASN][1000 genomes]
rs4846212	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4846213	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs55676616	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs58697740	0.81[AMR][1000 genomes]
rs61326491	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs61775885	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs61775887	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs61778376	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61778399	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs61778401	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs61778402	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs61778403	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs61778404	0.85[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs6541089	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6541090	0.91[ASN][1000 genomes]
rs6685895	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6696056	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs746881	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7524693	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7546364	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7546368	0.86[ASN][1000 genomes]
rs7547513	0.81[ASN][1000 genomes]
rs7553228	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7553935	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8019	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs912961	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs912962	0.84[ASN][1000 genomes]
rs912963	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9332414	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs946501	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs946502	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs946503	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs946504	0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2757722	chr1:10238070-10582554	Weak transcription Enhancers Genic enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	esv2758920	chr1:10238070-10582554	Strong transcription Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
3	nsv545381	chr1:10296452-10423988	Enhancers Genic enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
4	nsv817370	chr1:10305470-10697150	Weak transcription Flanking Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
5	nsv1008021	chr1:10363794-10802633	Strong transcription Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
6	esv2764192	chr1:10383734-10594186	Strong transcription Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12409933	KIF1B	cis	Thyroid	GTEx

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:10357600-10397000	Weak transcription	Fetal Thymus	thymus
2	chr1:10358800-10407000	Weak transcription	Primary B cells from cord blood	blood
3	chr1:10364600-10431000	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr1:10365200-10398400	Weak transcription	Fetal Heart	heart
5	chr1:10378200-10397200	Weak transcription	GM12878-XiMat	blood
6	chr1:10379400-10397200	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr1:10379800-10399400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr1:10380200-10399800	Weak transcription	Stomach Mucosa	stomach
9	chr1:10380200-10404800	Weak transcription	Psoas Muscle	Psoas
10	chr1:10380400-10399600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr1:10380400-10436600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
12	chr1:10380600-10401000	Weak transcription	A549	lung
13	chr1:10380600-10426400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr1:10381000-10436400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr1:10382800-10397200	Weak transcription	NHLF	lung
16	chr1:10385200-10396400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
17	chr1:10385200-10397200	Weak transcription	Primary T helper cells PMA-I stimulated	--
18	chr1:10385200-10436400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
19	chr1:10386000-10434800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
20	chr1:10386400-10396000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
21	chr1:10386400-10403000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
22	chr1:10386400-10421600	Weak transcription	Hela-S3	cervix
23	chr1:10386600-10396600	Weak transcription	Primary hematopoietic stem cells	blood
24	chr1:10386600-10397000	Weak transcription	Aorta	Aorta
25	chr1:10386600-10397000	Weak transcription	Colonic Mucosa	Colon
26	chr1:10386600-10399800	Weak transcription	Fetal Lung	lung
27	chr1:10386800-10397200	Weak transcription	NHEK	skin
28	chr1:10386800-10408600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
29	chr1:10387000-10396400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
30	chr1:10392000-10396800	Strong transcription	Fetal Intestine Small	intestine
31	chr1:10393200-10397800	Strong transcription	Brain Hippocampus Middle	brain
32	chr1:10393200-10415800	Strong transcription	Monocytes-CD14+_RO01746	blood
33	chr1:10393200-10431200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
34	chr1:10393400-10396400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
35	chr1:10393400-10402200	Strong transcription	Fetal Stomach	stomach
36	chr1:10393600-10397200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr1:10393600-10430800	Strong transcription	Primary neutrophils fromperipheralblood	blood
38	chr1:10393800-10406000	Strong transcription	Placenta	Placenta
39	chr1:10393800-10444600	Strong transcription	Cortex derived primary cultured neurospheres	brain
40	chr1:10394200-10395600	Strong transcription	Lung	lung
41	chr1:10394200-10397400	Strong transcription	Brain Anterior Caudate	brain
42	chr1:10394200-10397800	Strong transcription	Left Ventricle	heart
43	chr1:10394200-10398000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr1:10394200-10398400	Strong transcription	Brain Cingulate Gyrus	brain
45	chr1:10394200-10398400	Strong transcription	Brain Inferior Temporal Lobe	brain
46	chr1:10394200-10398400	Strong transcription	HSMMtube	muscle
47	chr1:10394200-10398800	Strong transcription	HUES6 Cell Line	embryonic stem cell
48	chr1:10394200-10399600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
49	chr1:10394200-10399800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
50	chr1:10394200-10400600	Strong transcription	Fetal Muscle Leg	muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links